The main problem here is that it's impossible to truly know which are safe at this point. I would bet the ones originaly used by the game outside the ASM Routines(0x4050-0x40c0) should be safe, but the area saved is widely unknown. The Variables are stored between People data on the OW and the Breeding Daycare store. But that area is large, and filled with used data. As they are indirectly referenced in-game, it may take a long while to find all possibilities out.

Wow, this is really bad...
I wish I could help, but I can barely do anything in ASM.